[Debian-med-packaging] Bug#924734: libbpp-seq-omics: FTBFS (dh_makeshlibs fails)

[Santiago Vila]

Package: src:libbpp-seq-omics
Version: 2.4.1-2
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
	cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
-- The CXX compiler identification is GNU 8.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- bpp-core 4.1.0 found:

[... snipped ...]

  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
@@ -1134,7 +1150,9 @@
  _ZTv0_n48_N3bpp25SimpleMafStatisticsResult8setValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi at Base 2.4.1
  _ZTv0_n48_N3bpp36CsvStatisticsOutputIterationListener14iterationStopsEv at Base 2.4.1
  _ZTv0_n48_NK3bpp12EdSymbolList11getAlphabetEv at Base 2.4.1
+ _ZTv0_n48_NK3bpp12SequenceMask11isRemovableEv at Base 2.4.1-2
  _ZTv0_n48_NK3bpp15SequenceQuality11isRemovableEv at Base 2.4.1
+ _ZTv0_n48_NK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1-2
  _ZTv0_n48_NK3bpp21AbstractMafStatistics9getResultEv at Base 2.4.1
  _ZTv0_n48_NK3bpp22SequenceWithAnnotation7getNameB5cxx11Ev at Base 2.4.1
  _ZTv0_n48_NK3bpp25AbstractSequenceContainer11getAlphabetEv at Base 2.4.1
@@ -1144,6 +1162,7 @@
  _ZTv0_n56_N3bpp16GtfFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
  _ZTv0_n56_N3bpp17SiteMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_N3bpp19AbstractMafIterator20addIterationListenerEPNS_17IterationListenerE at Base 2.4.1
+ _ZTv0_n56_N3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1-2
  _ZTv0_n56_N3bpp21BedGraphFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
  _ZTv0_n56_N3bpp22SequenceWithAnnotation7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n56_N3bpp25PolymorphismMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
@@ -1153,6 +1172,7 @@
  _ZTv0_n56_N3bpp34SiteFrequencySpectrumMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_N3bpp37FourSpeciesPatternCountsMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_NK3bpp12EdSymbolList4sizeEv at Base 2.4.1
+ _ZTv0_n56_NK3bpp12SequenceMask8isSharedEv at Base 2.4.1-2
  _ZTv0_n56_NK3bpp15BasicSymbolList4sizeEv at Base 2.4.1
  _ZTv0_n56_NK3bpp15SequenceQuality8isSharedEv at Base 2.4.1
  _ZTv0_n64_N3bpp16GffFeatureReader21getFeaturesOfSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
@@ -1160,12 +1180,14 @@
  _ZTv0_n64_N3bpp21BedGraphFeatureReader21getFeaturesOfSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
  _ZTv0_n64_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorIiSaIiEE at Base 2.4.1
  _ZTv0_n64_NK3bpp17SiteMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
+ _ZTv0_n64_NK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1-2
  _ZTv0_n64_NK3bpp22SequenceWithAnnotation11getCommentsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp25PolymorphismMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp28CharacterCountsMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp30SequenceDiversityMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp34SiteFrequencySpectrumMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp37FourSpeciesPatternCountsMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
+ _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1-2
  _ZTv0_n72_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZTv0_n72_N3bpp22SequenceWithAnnotation11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZTv0_n72_NK3bpp5Fastq12nextSequenceERSiRNS_8SequenceE at Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------

(The above is just how the build ends and not necessarily the most relevant part)

The build was made in my autobuilder with "dpkg-buildpackage -B"
and it also fails here:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-seq-omics.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.